City bus-and-subway boss Thomas Prendergast is being promoted to run the entire MTA, Gov. Cuomo announced today in a move that cheered transit advocates.

Prendergast, a longtime MTA executive, has been president of NYC Transit since November 2009. He’s also been president of the Long Island Rail Road and from 1991 to 1994 was NYC Transit’s senior vice president/subways — a job in which he was in charge of the entire subway system.

“I can’t imagine anyone having a better understanding of how the region’s vast system operates and the challenges that it faces,” Cuomo said in a statement.

The job will be a good cap to Prendergast’s 38-year transit career, said Robert Yaro, president of the Regional Plan Association.

“We have had four MTA directors in the last five years,” Yaro said. “If Tom can give us several years, it’s a terrific thing … We need a steady hand on the tiller.”

Transport Workers Union Local 100 — which is negotiating a new contract with the MTA — also welcomed Prendergast’s appointment.

“We’ve always had a good working relationship with Prendergast, despite a few flare-ups here and there,” said Local 100 spokesman Jim Gannon.

Prendergast has worked in public transit since 1975, when he joined the Chicago Transit Authority. He took his first MTA job in 1982.

Outside the MTA, Prendergast was in charge of the transit system in Vancouver during 2008 and 2009 and spent several years as an independent consultant to transit systems in North America, the United Kingdom and Asia.

Prendergast’s appointment has to be confirmed by the state Senate. He replaces Joseph Lhota, who left the MTA Jan. 1 to run for mayor.